The Day After
by Phoenix Nova
Summary: Colonel Sheppard's team arrives in orbit of Earth to find Earth's population a fraction of its former size. In an attempt to unravel the mystery, will Sheppard or his team survive, or with they join the billions of dead?
1. The Day After: Chapter 1

This chapter may be short, but I think you may be pleased . . . I hope!

* * *

Stargate Atlantis: The Day After

Chapter 1 - Something odd, indeed.

The Daedalus zipped through hyper space towards Earth.

Colonel Sheppard entered the mess, and sat down quietly, Rodney didn't notice him, as he was occupied. Rodney seemed anxious as he was pouring over some data, he obviously killing time with something that seemed important.

An airman walked in with a flash drive.

"Dr. McKay, this is the information you requested on the hyper drive diagnostic." the airman said handing Rodney the small device.

Taking it, Rodney plugged it in and began to compare the data. Rodney noticed something odd. "Hello, my pretty." Rodney said.

"You find something?" Colonel Sheppard asked.

Rodney wasn't expecting the comment, and nearly his tablet.

Wheeling around, Rodney asked "When did you come in?"

"Ten minutes ago, just before that airman walked in." Sheppard said, the returned to his original question. "You find something?"

"I think so, there was a huge power spike as we left the Pegasus galaxy." Rodney said.

"And that's bad right?" Sheppard asked.

"Well, I don't know. It could be anything from a ship to a black hole. But these energy readings are off the scale." Rodney prattled, he seemed freaked, and yet intrigued.

"All hands, this is the bridge, prepare to drop out of hyper space." Steven Caldwell advised. "Colonel Sheppard, have your team report to the bridge." Steven added.

"Come on Rodney, you can play with your toys when you chores are done." Colonel Sheppard said, Rodney gathered a few small things that were important to his diagnostic, and followed Sheppard out of the room.

Several seconds later and the Daedalus emerged from a hyper space window.

* * *

As the ship decelerated they viewed the blue marble floating in a sea of darkness trapped like some many stars in the distance.

Colonel Sheppard ad Dr. McKay arrived on the bridge, and yet their arrival seemed to go unnoticed.

"Well, check it again." Steven ordered, something was on his mind.

"Nothing, sir." Marks responded.

But then Steven looked in McKay's direction, finally they were being noticed.

"Dr. McKay, there seems to be a problem with some of Daedalus' systems, we can't contact Stargate Command, and our sensors are giving us some disturbing readings." Caldwell said.

About this time Jennifer Keller, Teyla, and Ronon entered the bridge.

"What is going on?" Teyla asked in reference to the confusion.

But Rodney didn't hear the question. "Well, let me see." Rodney said moving towards the panel for the sensors. But after examining the system for twenty minutes, he was unable to find any reason why the crew was unable to contact the SGC. Rodney looked at Marks. "What was wrong with the sensors?"

Marks looked at Caldwell, then back at Rodney. "Sensors detect a couple hundred thousand life signs on the planet." Marks said.

"I don't know about you, but the last time I checked, Earth's population was a hefty 6.4 billion." Caldwell said.

* * *

Any theories? Ideas? Chapter 2 is coming soon-ish.


	2. The Day After: Chapter 2

Thanks for the review, I had though of time travel, though a good idea, not where I was heading. This is more twisted and dastardly.

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**Stargate Atlantis: The Day After**

**Chapter 2 - World of Ruin**

After five exhaustive hours of looking at the sensors, and communications. Rodney delivered his report. "The communications, and sensors are working." Rodney said.

"But how could that be possible?" Caldwell asked.

"You think maybe there was an pandemic." Keller suggested.

Everyone turned to look at Jennifer. Hoping that Earth didn't suffer a global pandemic wiping out more than six billion people.

Marks came in on the comms.

"Colonel Caldwell, I've got some odd chatter on an AM frequency." Marks announced.

"Let's hear it, pipe it through." Caldwell requested, his attention wearing thin.

After a second a voice could be heard.

"My name is Robert Neville. I am a survivor living in New York City. I am broadcasting on all AM frequencies. I will be at the South street seaport every day at Midday, when the sun is highest in the sky. If you are out there -- If anyone is out there . . . I can provide food, I can provide shelter, I can provide security. If there's anybody out there -- anybody, please . . . you are not alone."

The broadcast ended and the speculation resumed.

"Who is this 'Robert Neville'?" Rodney McKay asked.

"I've heard of him, he's a virologist, or at least he was. He hasn't been heard from in a couple of years." Dr. Keller replied.

Colonel Sheppard was the voice of reason.

"There's no use wondering 'what happened?'. We need to go down there." Sheppard reasoned.

"What do you propose? We have no idea what went on down there over the last couple weeks, Earth may have been compromised by an alien organism or someone could have attacked." Caldwell surmised.

"All the more reason, I can take the puddle jumper we have in the port 302 bay down in stealth mode, and I'll go in HAZ-MAT." Colonel Sheppard compromised.

Caldwell gave in. "Gear up, and be ready to go in one hour. I'll have some teams assemble to go check out Stargate Command. But be advised, if something happens, we can't pluck you out of trouble, the transporters are being overhauled."

"Hopefully we won't need them." Sheppard commented, then nodded and escorted Rodney out.

Ronon was waiting outside to door. "What'd he say?" Ronon asked.

"We're going down to Earth, be ready to go in one hour." Colonel Sheppard replied. "Gear up we leave in one hour."

* * *

_**Daedalus **_**302 Bay - One Hour Later**

"Okay kids, keep you hands and feet inside the jumper at all times, until it has come to a complete stop." Sheppard said as he boarded the flying cigar-tube.

As the jumper left the bay, Colonel Caldwell gave some final orders.

"Stay in stealth mode, and do not engage anyone. You're there for reconnaissance." Caldwell reminded.

"Understood, sir." Sheppard confirmed.

The jumper entered Earth's atmosphere, and soon the New York City Skyline could be seen behind a fading sunlight.

"There it is, the City that never sleeps." Colonel Sheppard remarked.

Ronon gave a look of confusion, Teyla noticed.

"It means that most of the people are always awake." McKay explained.

"You don't know that." Sheppard retorted.

"Yeah, well, it sound like it needs a freakin' nap." Ronon said unimpressed.

Jennifer chuckled.

"You think that's bad, it's also called the 'Big Apple'." Sheppard added. "Over six million live there . . . or at least they used to live there."

Ronon chuckled at the nickname.

The jumper streaked into the expanse between skyscrapers.

"What the . . .?" Sheppard started.

"Is that what I think it is?" Jennifer asked.

Draped over a skyscraper was a giant covering with a symbol on it. Due to the decreased light they didn't notice what it was until the lights from the jumper hit it.

"Bio-hazard? When did this happen?" Sheppard asked.

Sheppard activated the link on his headset.

"Daedalus, this is Sheppard. We have a Bio-hazard here in Manhattan." Sheppard warned. "The place looks cleaned out, there's no way it was an epidemic." Sheppard advised.

"What about an attack from orbit?" Caldwell suggested.

"It doesn't look like it was an orbital attack either." Sheppard reported.

Sheppard brought up the HUD to check for life signs in the vicinity. There were about a dozen.

"Colonel Caldwell, we have some life signs not to far away, we're going to check it out." Sheppard advised, and brought the jumper in for a landing.

The door opened with a whine, and a thud.

Colonel Sheppard lead the way with his P-90, then Ronon, Teyla, Rodney and Jennifer.

They walked for three blocks before Sheppard pointed towards a building with a gaping hole in it. By now the fading sun had completely disappeared behind a nearby skyscraper.

"How could this have happened in the last few weeks?" Sheppard wondered aloud, but brushed it off with his military training, and filed everyone inside where the dozen life signs were detected.

The hallways were dark, muggy, and smelled of mold. Off in the distance there was a trickle echoing.

Sheppard looked at Teyla, who then stepped forward in an attempt to make contact.

"Hello?" Teyla called.

A low growl soon accompanied the trickle, then stopped.

Ronon didn't like it, he drew his gun and set it to kill.

"Do not be afraid, we are here to help." Teyla called, then it grew silent, the sound of the trickle seemed to grow louder, and amplify the silence.

Then it happened: a humanoid shape lunged from the darkness, shrieking.

It's eyes were bloodshot, it had no hair on it's head, and only wore severely tattered pants.

Ronon shot it down, and then the one screaming creature, who now lay dead on the ground, turned into a dozen screaming monsters emerging from the darkened corners of the building.

"Oh, crap." Rodney mourned.

"BACK TO THE JUMPER!" Shepard shouted as bullets began to fly.

Rodney and Jennifer lead the way, Sheppard, Teyla and Ronon provided withdrawing cover fire.

Once back onto the street, Sheppard and his team made a mad dash for the jumper.

"What was that?" Rodney asked.

"I don't know, but we're not waiting around to find out." Sheppard said.

"Maybe Caldwell wasn't too far off the mark, it was an alien attack." Ronon guessed.

"It does not matter. Run!" Teyla urged, then paused to spin around and fire on the encroaching mob. Several fell dead, but it seemed more had joined the ranks of the unknown creatures.

Soon the jumper could be seen, safety was not too far away. But then something fell on the jumper, a large object, and the impact caused an explosion that destabilized one of the surrounding buildings, causing a significant amount of debris to fall on it, further damaging it.

"You have got to be kidding." Rodney shrieked.

"We'll have to stand our ground." Sheppard said, but by now the numbers were closer to two or three dozen.

As the strange creatures got closer Sheppard prepared for his last stand.

* * *

don't ask me why there's suddenly a jumper in the Daedalus 302 bay, I'm working up to something.


	3. The Day After: Chapter 3

At long last a new chapter for The Day After. Thanks for your reviews, input, and otherwise.

**Stargate Atlantis - The Day After**

**Chapter 3 - A Mixed Bag**

Bullets continued to fly as the creatures close in almost dancing as they attempt to evade the weapons fire.

"Hold still!" Sheppard said as he fired a burst from his P-90, he didn't expect the creature to capitulate.

Then like manna from heaven, an SUV careens in. The driver looks at the oncoming mob, then at the five people expending their ammunition in an attempt to stay alive.

"GET IN!" the man snapped, pulling his dog to one side "Come on, Sam."

Sheppard didn't hesitate, he climbed in. McKay was next, Jennifer was pulled into the vacant seat, Ronon and Teyla held onto the sides of the SUV, and kept firing.

The driver hit the gas, and sped away, the strange creatures gave chase, but soon only their shrieks could be heard.

"We have to get back to my compound, now!" the man said, he seemed to be military, so he didn't say much all the way back.

After twenty minutes they pulled up to a building, and he filed everyone out of the SUV, grabbed a bottle of something and directed everyone through a door at the top pf some stairs. He was the last to follow, and as he walked up the stairs he sprayed a clear liquid from the jug he grabbed from his vehicle, then closed and locked the door behind him.

He stood there, at the door, just thinking. Then turned towards the one he assumed was in command.

"Where have you been?" the man asked.

"It's a long story." Sheppard replied. Then asked a question of his own.

"What happened here? It wasn't like this last month!" Sheppard corrected.

"Last Month? K.V. hit two and a half years ago. It killed ninety percent of the planets population, you had a close run-in with the infected that it didn't kill." the man snapped.

"Two years? Alright, let's start from the top. I'm Lt. Colonel John Sheppard."

The man remembered his humanity, and then introduced himself. "Lt. Colonel Robert Neville." they saluted.

Jennifer chimed in. "Tell me more about 'K.V.'. What is it?" Sheppard introduce their medical officer.

"This is Dr. Jennifer Keller."

Robert took a deep breath. "It was developed by Dr. Alice Krippen to be a cure for cancer -- To save mankind." Robert explained.

"That's irony for you." Sheppard remarked.

"It was basically a genetically altered Measles virus." Robert summarized.

"They're vulnerable to UV light." Robert explained, he seemed to be reading McKay's mind.

"And tough to kill." Ronon added.

Teyla discreetly suggested contacting the Daedalus. Sheppard excused himself.

"Daedalus, this is Sheppard."

"Sheppard? We were starting to get worried, we lost the beacon in the jumper." Caldwell replied.

"It was kind of destroyed. Look the bottom line is, there's a global pandemic." Sheppard explained.

"That explains the diminished life signs." Caldwell concluded. "I hope there is good news?"

"Kind of hoping that myself." Sheppard replied.

"What's the situation, Colonel?" Caldwell finally asked.

"There are a lot of infected people down here. But we did make contact with a survivor." Sheppard added.

"In that case, have Dr. Keller check you out, we'll work on getting the transporter back up and running." Caldwell promised.

At those words Rodney burst in.

"I think I have something you should know about." Rodney announced.

"And that would be . . ." Sheppard invited.

"You remember me mentioning a momentary power spike when we left the Pegasus galaxy?" Rodney asked.

"Yeah?" Sheppard asked, encouraging Rodney to make his point.

"The power spike was a freak accident. There was a one in a trillion cosmic event that acted like Merlin's "out-of-phase" technology, and since we were in subspace when that power surge occurred. . ."

"Rodney!" Sheppard stated finally.

"We're in an alternate Universe!"

And you all thought it was a time travel thing. Good guess. But I chose an alternate route.

Thanks for reading, and maybe chapter 4 will be up soon.


End file.
